Data Protection Manager 2012 - Inconsistent when backing up Deduplicated File Server

Question

Protected Server
Server 2012 File Server with Deduplication running on Data drive
DPM Server
Server 2012
Data Protection Manager 2012 Service Pack 1
We just recently upgraded our DPM server from DPM 2010 to DPM 2012 primarily because it is supposed to support Data Deduplication. Our primary File server that holds our home directories etc. is limited on space and was quickly running low so just after
we got DPM 2012 in place we optimized the drive on the file server which compressed the data about 50%. Unfortunately shortly after enabling deduplication the protected shares on the deduplicated volume are getting a Replica is Inconsistent error.
I continually get Replica is Inconsistent for the Server that has deduplication running on it. All of the other protected servers are being protected as they should be. I have run a consistency check multiple times probably about 10 times and it keeps going
back to Replica is inconsistent. The replica volume shows that it is using 3.5 TB and the Actual protect volume is 4TB in size and has about 2.5 TB of data on it with Deduplication enabled.
This is the details of the error
Affected area:   G:\
Occurred since: 1/12/2015 4:55:14 PM
Description:        The replica of Volume G:\ on E****.net is inconsistent with the protected data source. All protection activities for data source will fail until the replica is synchronized with
consistency check. You can recover data from existing recovery points, but new recovery points cannot be created until the replica is consistent.
For SharePoint farm, recovery points will continue getting created with the databases that are consistent. To backup inconsistent databases, run a consistency check on the farm. (ID 3106)
More information
Recommended action: 
Synchronize with consistency check.
Run a synchronization job with consistency check...
Resolution:        
To dismiss the alert, click below
Inactivate
Steps taken to resolve - I’ve spent some time doing some searches and haven’t found any solutions to what I am seeing. I have the data deduplication role installed on the DPM server which has been the solution for many people seeing similar issues. I have
also removed that role and the added it back. I have also removed the protected server and added it back to the protection group. It synchronizes and says consistent then after a few hours it goes back to inconsistent. When I go to recovery it shows that I
have recovery points and it appears that I can restore but because the data is inconstant I don’t feel I can trust the data in the recovery points. Both the protected server and the DPM servers’ updates are managed via a WSUS server on our network.
You may suggest I just un-optimize the drive on the protected server however after I have optimized the drive it takes a large amount more of space to un-optimize it (Anyone know why that is) anyways the drive isn’t large enough to support un-optimization.
If anyone has any suggestions I would appreciate any help. Thanks in advanced.

Answer 1

Ok I ran a consistency check and it completed successfully with the following message. However after a few minutes of it showing OK it now shows Replica is Inconsistent again.
Type: Consistency check
Status: Completed
Description: The job completed successfully with the following warning:
 An unexpected error occurred while the job was running. (ID 104 Details: Cannot create a file when that file already exists (0x800700B7))
 More information
End time: 2/3/2015 11:19:38 AM
Start time: 2/3/2015 10:34:35 AM
Time elapsed: 00:45:02
Data transferred: 220.74 MB
Cluster node -
Source details: G:\
Protection group members: 35
 Details
Protection group: E*
Items scanned: 2017709
Items fixed: 653
There was a log for a failed synchronization job from yesterday here are the details of that.
Type: Synchronization
Status: Failed
Description: The replica of Volume G:\ on E*.net is not consistent with the protected data source. (ID 91)
 More information
End time: 2/2/2015 10:04:01 PM
Start time: 2/2/2015 10:04:01 PM
Time elapsed: 00:00:00
Data transferred: 0 MB
Cluster node -
Source details: G:\
Protection group members: 35
 Details
Protection group: E*